Cross-kingdom patterns of alternative splicing and splice recognition
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CitationMcGuire, Abigail M., Matthew D. Pearson, Daniel E. Neafsey, and James E. Galagan. 2008. Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biology 9(3): R50.
AbstractBackground: Variations in transcript splicing can reveal how eukaryotes recognize intronic splice
sites. Retained introns (RIs) commonly appear when the intron definition (ID) mechanism of splice
site recognition inconsistently identifies intron-exon boundaries, and cassette exons (CEs) are
often caused by variable recognition of splice junctions by the exon definition (ED) mechanism. We
have performed a comprehensive survey of alternative splicing across 42 eukaryotes to gain insight
into how spliceosomal introns are recognized.
Results: All eukaryotes we studied exhibit RIs, which appear more frequently than previously
thought. CEs are also present in all kingdoms and most of the organisms in our analysis. We
observe that the ratio of CEs to RIs varies substantially among kingdoms, while the ratio of
competing 3' acceptor and competing 5' donor sites remains nearly constant. In addition, we find
the ratio of CEs to RIs in each organism correlates with the length of its introns. In all 14 fungi we
examined, as well as in most of the 9 protists, RIs far outnumber CEs. This differs from the trend
seen in 13 multicellular animals, where CEs occur much more frequently than RIs. The six plants
we analyzed exhibit intermediate proportions of CEs and RIs. Conclusion: Our results suggest that most extant eukaryotes are capable of recognizing splice
sites via both ID and ED, although ED is most common in multicellular animals and ID predominates
in fungi and most protists.
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